Address sample callrate filtering

[mike-w-wilson]

The current seqr sample qc pipeline does not apply hard filters in the get_qc_mt function: https://github.com/broadinstitute/gnomad_methods/blob/0b8e1007aacabcb81e4093d9e315ac6f7c92651b/gnomad/sample_qc/pipeline.py#L106 . Should we add it in as the UKBB does? We also do not flag internal exomes for low callrate.

[gtiao]

I think it's a good idea to flag these, although I don't think the seqr sample QC function should remove samples that fail hard filters. We should flag internal exomes for low callrate. G.

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On Thu, Jun 4, 2020 at 3:57 PM Mike Wilson ***@***.***> wrote: The current seqr sample qc pipeline does not apply hard filters in the get_qc_mt function: https://github.com/broadinstitute/gnomad_methods/blob/0b8e1007aacabcb81e4093d9e315ac6f7c92651b/gnomad/sample_qc/pipeline.py#L106 . Should we add it in as the UKBB does? We also do not flag internal exomes for low callrate. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#13>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNSGHSWBCZV3ZSYVLYVBEDRU74CTANCNFSM4NS55WCQ> .